ribosomeReleaseScore {ribosomeProfilingQC} | R Documentation

## Ribosome Release Score (RRS)

### Description

RRS is calculated as the ratio of translational efficiency in the CDS with RPFs in the 3'UTR.

### Usage

    ribosomeReleaseScore(
      cdsTE,
      utr3TE,
      CDSsampleOrder,
      UTR3sampleOrder,
      pseudocount = 0,
      log2 = FALSE
    )

### Arguments

`cdsTE, utr3TE` | Translational efficiency of CDS and UTR3 region. Output of translationalEfficiency
`CDSsampleOrder, UTR3sampleOrder` | Sample order of cdsTE and utr3TE. The parameters are used to make sure that the order of CDS and UTR3 in TE is corresponding samples.
`pseudocount` | The number will be add to sum of reads count to avoid X/0.
`log2` | Do log2 transform or not.

### Value

A vector of RRS.

### Examples

    ## Not run:
    path <- system.file("extdata", package="ribosomeProfilingQC")
    RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE)
    RNAs <- dir(path, "mRNA.*?\\.[12].bam$", full.names=TRUE)
    gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
    cvgs <- coverageDepth(RPFs, RNAs, gtf)
    cvgs.utr3 <- coverageDepth(RPFs, RNAs, gtf, region="utr3")
    TE90 <- translationalEfficiency(cvgs, window = 90)
    TE90.utr3 <- translationalEfficiency(cvgs.utr3, window = 90)
    rrs <- ribosomeReleaseScore(TE90, TE90.utr3)

    ## End(Not run)

[Package ribosomeProfilingQC version 0.99.9 Index]